Thanks to my good friend Melkor for helping me to understand! (Melkor is another user on inreview.com forums and helped me to write this. Oh, and dreamweaver )

NEO'S DEATH:
At the end of M3, you see all the Smiths lined up and one waiting to fight Neo. The one Smith is Smith imprinted over the Oracle. The others are all the remaining people plugged into the Matrix. Smith took over everyone in the matrix, this does NOT lead to them being instantly killed, he simply takes over the mind and the computerized self of the human.

When Neo begins to fight Smith, he thinks he needs to destroy Smith in order to end the war. However, the Oracle lets Neo know that the only way to defeat Smith is to concede defeat, hence the reason the Smith program addresses Neo as 'Neo' and not 'Mr Andersen' as Smith usually does. This is unprecedented and is the Oracle influencing Smith in order to explain to Neo what must be done. Neo then realises that by letting Smith win, the aspect of the equation relating to two of them will be unbalanced, and so the Smith element will not survive. This goes back to what the oracle said at the beginning of Revolutions, 'He is you. Your opposite, your negative, the result of the equation trying to balance itself out'.

Oracle-Smith said whatever has a beginning has an end. And in the end, Neo realized that there was only one way to end smith, and that meant his own end. This all goes back to the quote on top of the oracle's doorway. "know thyself". And when Neo finally knew himself, he finally knew what he should do, and he was finally able to see beyond the choice because he now understood his choice (you cannot see beyond the choices you do not understand).

THE CONFUSION?!?!?!
Smith, as he had the skill of sight from the Oracle, predicted that Neo would fall, but thus, didn't see past his choice in killing him and therefore didn't foresee his own fall. Smith is confused because of what he's saying. The oracle (as I said before) is influencing him. She had planned this, she stayed to make sure that when the time came, she could send that message to Neo. This is why she made no effort to run from him when Smith came to her apartment.

Neo dies, but the One then returns to the source, allowing the temporary dissemination of the code he carries as mentioned by the Architect in Reloaded. This allows the matrix to be reloaded, only this time with a substantial difference: anyone who wants to leave the matrix can do, and this time Zion will not be destroyed and they can live in the 'real' world in peace.

When Sati says 'Will we see Neo again?" She is referring to what will happen if the peace does not last and the equation is unbalanced. They will need to bring the One back, although, Neo is dead, therefore meaning someone else must become the One.

NEO'S EYES:
Neo is the One. There could be one million and one reasons why he can see the things he sees. I believe it is because he is linked to the source, he could see all the machines and wire because they are all linked to the source too. He could also see everything that has a purpose (eg Smith - purpose is to destroy Neo) He couldn't see Trinity because she has no purpose, she is a normal human.

WHY SMITH IS A THREAT TO THE MACHINES:
There are many ways Smith can get to the Real world. Imprinting over people with a link out (members of hover crafts) and imprinting people like the Trainman and the merovingian. An the end, we assume that Smith has taken over every human in the world, if he has not, that he will do so is inevitable. This includes the Trainman and Merv, thus leading to the link to the Machine world AND the Matrix, leaving Smith free to move between the two. Smith's power, like Neo's, is linked to the Source. As such, Smith can influence the machine world just as Neo can. He could control the machines as Neo did the Sentinels, through, with millions of Smiths, he could do a lot more. But then, why did he not just go to the machine world in the first place and kill everyone in the Real world? Because Smith's purpose is to destroy Neo, "We've been here before, you and I. Remember? I do. I think of nothing else". He is obsessed with killing Neo and therefore can not do anything until his purpose is complete.

SMITH CALLING THE ORACLE 'MUM'
This is a play on words. He is being sarcastic, he is referring to the Oracle as 'The mother of the matrix' therefore meaning everything and everyone in the matrix is her 'child'. This confused many, some saying it was Seraph under Smith calling her mum, but Seraph is defiantly not the Oracle's son. She has not real children.

THE ORACLE:
The 6th version of the Matrix was planned to be just as all the others: a continuing cycle of birth, life and death designed to keep humans under control. The Oracle changed this, and that was what the Architect was referring to at the end of Revolutions.

The One has died before Morpheus said this in the first Matrix film. This has obviously occurred in all prior versions of the matrix when the One has gone to the Source and chosen the door that Neo did NOT choose this time. The Oracle has planned this from beginning. She has decided that change is for the better and therefore plays her 'dangerous game' in order to attempt to obtain peace.

Instead of simply guiding the One, she makes small changes, we see many signs of this. She brought Trinity into the picture, she told her she would fall in love with Neo, thus leading to the connection growing stronger and hence - him choosing to save her over the recreation of Zion. She told Niobe that she would have to choose to help neo or not, ensuring that Neo got the Logos and flew to 01, to make the deal and kill Smith etc.

CANDY EXPLAINED:

The candy is symbolic of the Oracle's human traits. She was created to delve into the human psyche, and has human traits as a consequence. Ergo, she can experience taste. The Oracle has grown to appreciate human past-times eg - eating, cooking etc.

This is the reason that she feel the future needs to be approached 'together'- she wants peace, a consequence of her quasi-dualistic nature. The candy has numerous connotations.
Choice is definitely one of them. We see this when she offers the candy to Neo and he says "Do you already know if I'm going to take it". This comment leads on to a more important matter - That we have already made all our choices in life, now we have to understand why we made them. Without the candy, we wouldn't have got onto the subject

All except that the Matrix was reloaded. It wasn't. It was just repaired to before Smith took over. And I'm pretty sure that Smith taking over Neo didn't kill them. It was the energy or program that the machines loaded into Neo.

__________________"The MTV Movie Awards are a systemic anomaly inherent to the programming of the Matrix. Although the transport process has altered your consciousness, you irrevocably remain human. Ergo, concordantly, vis-a-vis... You know what? I have no idea what the hell I'm saying. I just thought it would make me sound cool."
-The Architect AKA Larry

when Neo became a Smith, the equation was unbalanced because Neo (+1) joined with Smith (-1) = 0 so they both died. And yes, when neo died and returned to the source, he reloaded the matrix as it had in all the previous matrixs. The architect said the other door led to the source and when all the previous ones went to the source, it reloaded the matrix. The official site TELLS us that...

Originally posted by Mistique when Neo became a Smith, the equation was unbalanced because Neo (+1) joined with Smith (-1) = 0 so they both died. And yes, when neo died and returned to the source, he reloaded the matrix as it had in all the previous matrixs. The architect said the other door led to the source and when all the previous ones went to the source, it reloaded the matrix. The official site TELLS us that...

Hope that helps

Which of your reply does the official site say?

And when Neo is taken over by Smith, it doesn't balance the equation. Smith's existence balanced it. Smith taking him over made Neo a negative, unbalancing it. They then loaded some program into Neo, which then destroyed them. And the Matrix wasn't reloaded. It was repaired.

__________________"The MTV Movie Awards are a systemic anomaly inherent to the programming of the Matrix. Although the transport process has altered your consciousness, you irrevocably remain human. Ergo, concordantly, vis-a-vis... You know what? I have no idea what the hell I'm saying. I just thought it would make me sound cool."
-The Architect AKA Larry

Hi Mistique, Agree on most of your subjects, its mostly what conclusions I got, just two things the first one is not a disagreement more just a change of wording-

1) You said that there where five previous versions of the matrix (this point confuses a lot of people), there are not five previous versions of the matrix but five previous versions of the anomaly (the one), the Architect had made two versions of the matrix (perfect worlds the human did not accept) prior to the current one so there are three versions of the matrix and five versions the anomaly. As I say not a disagreement but more a change in the wording.

2) This is a point that is and will continue to be agreed for a long time, but I believe that the matrix was not reloaded, but instead just continued, two things bring me to this, one is the black cat, which signifies a change in the current matrix, not a reload, if it was reloaded then there would be not point in the black cat being in the third film. And secondly there would be no point in the machines reloading the matrix as this is only done to control the human and since peace is been declared then the machine do not need to control the humans, and machine do not do nothing that is unnecessary because it is not logical and machine work on logic.

Godfather, there are five earlier versions of the Matrix, but three different types. The first type failed, then the current one was created. It has been reloaded five times, making five versions.

__________________"The MTV Movie Awards are a systemic anomaly inherent to the programming of the Matrix. Although the transport process has altered your consciousness, you irrevocably remain human. Ergo, concordantly, vis-a-vis... You know what? I have no idea what the hell I'm saying. I just thought it would make me sound cool."
-The Architect AKA Larry

The unknown> that was my theory also. people are now telling me that there were 5 ones, but only 3 version of the matrix. What I don't understand is how there's 3, the perfect one that failed, this one, and what else? The architect's speech about this being the 6th time we've destroyed zion and we are becomming efficiantly good at it sort of gave me the impression that the matrix was to be reloaded.

Oh, and I don't think I did read it on the site, must have read it somewhere else because now I doubt that they would say that. Sorry!!! I'm really good at opening my big mouth today... not havin a good one

I still sort of don't understand the theory of there being 3 versions of the matrix and not 5.... but then, the architect said something about the 'perfect' matrix but it can't be, because there were 5 ones and the matrix was reloaded when they reached the source, so that would mean it's another version. Just because the black cat crossed the passed in the end of revos, doesn't prove that it wasn't reloaded, it was changed AND reloaded was it not????

Did you notice the way the architect explained about the versions, he said "I prefer to count from the emersions of on intergral anomaly to the emersions of the next, in which case this is the sixth version".The plot has been explained for you all and I understand and agree with it fully.

BUT I don't think Smith died because they cancelled each other out, I reckon Smith died because he no longer has a "purpose".
Smith himself said "Without purpose, we would not exist" and he also said "We are here because of YOU Mr. Anderson we're here to take from you what you tried to take from us.....PURPOSE".

The Architect made "The Perfect World" Matrix, people didnt' except it so he made a second Matrix with imperfection. People again didn't except it. The Oracle studied humans and figured out the human need choice. The Architect made a Third Matrix this time giving people a choice: Except the Program or don't. Even though the choice was made at a subconcious level the humans generally "decided" to stay plugged in. So now we have 3 version of the Matrix. In Matrix 3.0 there was a man, the One, who went back to the source and reloaded the Matrix and rebuilt Zion. Now we have Matrix 3.1 and the same thing happened untill Matrix 3.5 when Neo came about.

The Matrix was not reloaded we know this from the black cat at the end. Ask yourself this "Did the Matrix reload when we first saw the black cat?" No. So why should it reload this time. Also, when we see Neo's dead body glowing that shows that the anomally is still in it and not returned to the source which also means Matrix 5.0 was not reloaded.